ISAcreator creates multiple Protocols with the same Name if they have the same type

[proccaserra]

reported by Steffen:
if an ISA configuration defines several tables using the same Protocol Type (say 'data transformation'), ISAcreator upon creation of the assay tables, automatically creates the relevant Protocol objects in the investigation file. The problem is that ISAcreator will create 'duplicates' as "Protocol Name" value is set using the 'Protocol Type':

Fix: -> unique 'Protocol Name' but keep the Protocol Type as supplied by the configuration

[proccaserra]

Also reported as a nuisance by Metabolights

[eamonnmag]

do you want to append the assay type to the protocol name? fixing is easy, it's just a matter of deciding how to name things.

[proccaserra]

we need a counter as we could have 4 assay tables, for instance 2 NMR assays and 2 MS assays, all protocols used in each could share types but be different. Counting the number of assay type would allow to unique the protocol. Note: modulation could be achieved too with uniquing the Protocol Name (as those are set based on 'Protocol Type' found in the configuration